/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project
*
* Contact: cdk-devel@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk.io;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.Iterator;
import java.util.StringTokenizer;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.MDLRXNFormat;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Reads a molecule from an MDL RXN file {@cdk.cite DAL92}.
*
* @cdk.module io
* @cdk.githash
*
* @author Egon Willighagen
* @cdk.created 2003-07-24
*
* @cdk.keyword file format, MDL RXN
*/
@TestClass("org.openscience.cdk.io.MDLRXNReaderTest")
public class MDLRXNReader extends DefaultChemObjectReader {
BufferedReader input = null;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(MDLReader.class);
/**
* Contructs a new MDLReader that can read Molecule from a given Reader.
*
* @param in The Reader to read from
*/
public MDLRXNReader(Reader in) {
this(in, Mode.RELAXED);
}
public MDLRXNReader(Reader in, Mode mode) {
if (in instanceof BufferedReader) {
input = (BufferedReader)in;
} else {
input = new BufferedReader(in);
}
super.mode = mode;
}
public MDLRXNReader(InputStream input) {
this(input, Mode.RELAXED);
}
public MDLRXNReader(InputStream input, Mode mode) {
this(new InputStreamReader(input), mode);
}
public MDLRXNReader() {
this(new StringReader(""));
}
@TestMethod("testGetFormat")
public IResourceFormat getFormat() {
return MDLRXNFormat.getInstance();
}
@TestMethod("testSetReader_Reader")
public void setReader(Reader input) throws CDKException {
if (input instanceof BufferedReader) {
this.input = (BufferedReader)input;
} else {
this.input = new BufferedReader(input);
}
}
@TestMethod("testSetReader_InputStream")
public void setReader(InputStream input) throws CDKException {
setReader(new InputStreamReader(input));
}
@TestMethod("testAccepts")
public boolean accepts(Class classObject) {
Class[] interfaces = classObject.getInterfaces();
for (int i=0; i<interfaces.length; i++) {
if (IChemModel.class.equals(interfaces[i])) return true;
if (IChemFile.class.equals(interfaces[i])) return true;
if (IReaction.class.equals(interfaces[i])) return true;
if (IReactionSet.class.equals(interfaces[i])) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
/**
* Takes an object which subclasses IChemObject, e.g.Molecule, and will read
* this (from file, database, internet etc). If the specific implementation
* does not support a specific IChemObject it will throw an Exception.
*
* @param object The object that subclasses
* IChemObject
* @return The IChemObject read
* @exception CDKException
*/
public IChemObject read(IChemObject object) throws CDKException {
if (object instanceof IChemFile) {
return readChemFile((IChemFile)object);
} else if (object instanceof IChemModel) {
return readChemModel((IChemModel)object);
} else if (object instanceof IReactionSet) {
return readReactionSet((IReactionSet)object);
} else if (object instanceof IReaction) {
return readReaction(object.getBuilder());
} else {
throw new CDKException("Only supported are Reaction, ReactionSet, ChemModel and ChemFile, and not " +
object.getClass().getName() + "."
);
}
}
@TestMethod("testAccepts")
public boolean accepts(IChemObject object) {
if (object instanceof IReaction) {
return true;
} else if (object instanceof IChemModel) {
return true;
} else if (object instanceof IChemFile) {
return true;
} else if (object instanceof IReactionSet) {
return true;
}
return false;
}
/**
* Read a ChemFile from a file in MDL RDF format.
*
* @param chemFile The IChemFile
* @return The IChemFile that was read from the RDF file.
*/
private IChemFile readChemFile(IChemFile chemFile) throws CDKException {
IChemSequence chemSequence = chemFile.getBuilder().newChemSequence();
IChemModel chemModel = chemFile.getBuilder().newChemModel();
chemSequence.addChemModel(readChemModel(chemModel));
chemFile.addChemSequence(chemSequence);
return chemFile;
}
/**
* Read a IChemModel from a file in MDL RDF format.
*
* @param chemModel The IChemModel
* @return The IChemModel that was read from the RDF file
*/
private IChemModel readChemModel(IChemModel chemModel) throws CDKException {
IReactionSet setOfReactions = chemModel.getReactionSet();
if (setOfReactions == null) {
setOfReactions = chemModel.getBuilder().newReactionSet();
}
chemModel.setReactionSet(readReactionSet(setOfReactions));
return chemModel;
}
/**
* Read a IReactionSet from a file in MDL RDF format.
*
* @param setOfReactions The IReactionSet
* @return The IReactionSet that was read from the RDF file
*/
private IReactionSet readReactionSet(IReactionSet setOfReactions) throws CDKException {
IReaction r = readReaction(setOfReactions.getBuilder());
if (r != null) {
setOfReactions.addReaction(r);
}
String str;
try {
String line;
while ((line = input.readLine()) != null) {
logger.debug("line: ", line);
// apparently, this is a SDF file, continue with
// reading mol files
str = new String(line);
if (str.equals("$$$$")) {
r = readReaction(setOfReactions.getBuilder());
if (r != null) {
setOfReactions.addReaction(r);
}
} else {
// here the stuff between 'M END' and '$$$$'
if (r != null) {
// ok, the first lines should start with '>'
String fieldName = null;
if (str.startsWith("> ")) {
// ok, should extract the field name
str.substring(2); // String content =
int index = str.indexOf("<");
if (index != -1) {
int index2 = str.substring(index).indexOf(">");
if (index2 != -1) {
fieldName = str.substring(index+1,index+index2);
}
}
// end skip all other lines
while ((line = input.readLine()) != null && line.startsWith(">")) {
logger.debug("data header line: ", line);
}
}
if (line == null) {
throw new CDKException("Expecting data line here, but found null!");
}
String data = line;
while ((line = input.readLine()) != null &&
line.trim().length() > 0) {
if (line.equals("$$$$")) {
logger.error("Expecting data line here, but found end of molecule: ", line);
break;
}
logger.debug("data line: ", line);
data += line;
// preserve newlines, unless the line is exactly 80 chars; in that case it
// is assumed to continue on the next line. See MDL documentation.
if (line.length() < 80) data += System.getProperty("line.separator");
}
if (fieldName != null) {
logger.info("fieldName, data: ", fieldName, ", ", data);
r.setProperty(fieldName, data);
}
}
}
}
} catch (CDKException cdkexc) {
throw cdkexc;
} catch (Exception exception) {
String error = "Error while parsing SDF";
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
}
return setOfReactions;
}
/**
* Read a Reaction from a file in MDL RXN format
*
* @return The Reaction that was read from the MDL file.
*/
private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
logger.debug("Reading new reaction");
int linecount = 0;
IReaction reaction = builder.newReaction();
try {
input.readLine(); // first line should be $RXN
input.readLine(); // second line
input.readLine(); // third line
input.readLine(); // fourth line
} catch (IOException exception) {
logger.debug(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int reactantCount = 0;
int productCount = 0;
try {
String countsLine = input.readLine();
linecount++;
if (countsLine == null) {
return null;
}
logger.debug("Line " + linecount + ": " + countsLine);
if (countsLine.startsWith("$$$$")) {
logger.debug("File is empty, returning empty reaction");
return reaction;
}
/* this line contains the number of reactants
and products */
StringTokenizer tokenizer = new StringTokenizer(countsLine);
reactantCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + reactantCount + " reactants in file");
productCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + productCount + " products in file");
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
// now read the reactants
try {
for (int i=1; i<=reactantCount; i++) {
StringBuffer molFile = new StringBuffer();
input.readLine(); // announceMDLFileLine
String molFileLine = "";
do {
molFileLine = input.readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
} while (!molFileLine.equals("M END"));
// read MDL molfile content
MDLReader reader = new MDLReader(
new StringReader(molFile.toString()));
IMolecule reactant = (IMolecule)reader.read(
builder.newMolecule()
);
// add reactant
reaction.addReactant(reactant);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while reading reactant", exception);
}
// now read the products
try {
for (int i=1; i<=productCount; i++) {
StringBuffer molFile = new StringBuffer();
input.readLine(); // String announceMDLFileLine =
String molFileLine = "";
do {
molFileLine = input.readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
} while (!molFileLine.equals("M END"));
// read MDL molfile content
MDLReader reader = new MDLReader(
new StringReader(molFile.toString()),
super.mode
);
IMolecule product = (IMolecule)reader.read(
builder.newMolecule());
// add reactant
reaction.addProduct(product);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while reading products", exception);
}
// now try to map things, if wanted
logger.info("Reading atom-atom mapping from file");
// distribute all atoms over two AtomContainer's
IAtomContainer reactingSide = builder.newAtomContainer();
Iterator molecules = reaction.getReactants().molecules().iterator();
while (molecules.hasNext()) {
reactingSide.add((IMolecule)molecules.next());
}
IAtomContainer producedSide = builder.newAtomContainer();
molecules = reaction.getProducts().molecules().iterator();
while (molecules.hasNext()) {
producedSide.add((IMolecule)molecules.next());
}
// map the atoms
int mappingCount = 0;
// IAtom[] reactantAtoms = reactingSide.getAtoms();
// IAtom[] producedAtoms = producedSide.getAtoms();
for (int i=0; i<reactingSide.getAtomCount(); i++) {
for (int j=0; j<producedSide.getAtomCount(); j++) {
IAtom eductAtom = reactingSide.getAtom(i);
IAtom productAtom = producedSide.getAtom(j);
if (eductAtom.getID() != null &&
eductAtom.getID().equals(productAtom.getID())) {
reaction.addMapping(
builder.newMapping(eductAtom, productAtom)
);
mappingCount++;
break;
}
}
}
logger.info("Mapped atom pairs: " + mappingCount);
return reaction;
}
@TestMethod("testClose")
public void close() throws IOException {
input.close();
}
}